In 2199, five years after the Gamilons began an invasion of Earth, the planet has been ravaged by the aliens’ bombs. The remnants of humanity have fled underground to escape the irradiated surface. One day, former pilot Susumu Kodai discovers a capsule sent from the planet Iscandar that tells of a device that can remove the radiation from the Earth’s surface. The Earth Defense Force rebuilds the battleship Yamato with a new type of propulsion system to make the 148,000 light year trip to Iscandar in hopes of saving the Earth. Within one year, the radiation will drive the rest of humanity to extinction.

Paleontologist Robert Trenton (Dean Cain) is called to Northeastern Antarctica near the Indian Ocean to help the FBI build an underground maximum-security military base and prison for the world’s most dangerous criminals and terrorists. The prison is dubbed “New Alcatraz” by the staff. While building the prison, the staff accidentally awaken and unleash a prehistoric Boa Constrictor from its 200 year hibernation. The snake escapes unnoticed until the staff notice a massive hole chewed in the five-foot thick concrete walls. Soon, the staff, and prisoners begin disappearing as they are brutally hunted and eaten by the snake. The FBI agents, Trenton and the rest of the prisoners try to escape, but are hampered as they don’t have many weapons. They begin to give up hope as most of the survivors die. However, Trenton manages to blow up the snake underground before escaping to the surface with the only other survivor being his wife.